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Information on EC 2.7.7.6 - DNA-directed RNA polymerase and Organism(s) Escherichia coli and UniProt Accession P0A8V2
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2.7.7.6 DNA-directed RNA polymeraseIUBMB Comments
Catalyses DNA-template-directed extension of the 3'- end of an RNA strand by one nucleotide at a time. Can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. See also EC 2.7.7.19 (polynucleotide adenylyltransferase) and EC 2.7.7.48 (RNA-directed RNA polymerase).
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Word Map
- 2.7.7.6
- chromatin
- histone
- rrna
- strand
-
rnaps
- nucleosome
- tata
- drosophila
-
pausing
- pre-mrnas
- tbp
-
nucleolar
- bacteriophage
-
polyadenylation
-
single-stranded
-
cyclin-dependent
-
holoenzyme
- cyclin
-
spacers
- helicase
-
fidelity
- polya
-
coactivator
-
protein-coding
-
transactivation
- adenovirus
- xenopus
- ribonucleoproteins
-
sequence-specific
-
stall
-
pause
-
chip-seq
- vaccinia
-
multisubunit
-
ribozyme
- heptapeptide
- duplex
-
h3k4me3
-
spliceosome
- nucleoplasm
-
run-on
-
supercoiled
-
trimethylation
-
subcomplexes
-
exonuclease
- heterochromatin
-
translesion
- medicine
- primase
- molecular biology
- analysis
- diagnostics
- drug development
-
misincorporation
-
proofread
- synthesis
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
rna polymerase ii, pol ii, t7 rna polymerase, rna polymerase i, pol iii, rna polymerase iii, pol i, rnapii, rnap ii, dna-dependent rna polymerase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
C RNA formation factors
-
-
-
-
chloroplast soluble RNA polymerase
-
-
-
-
deoxyribonucleic acid-dependent ribonucleic acid polymerase
-
-
-
-
DNA-dependent ribonucleate nucleotidyltransferase
-
-
-
-
DNA-dependent RNA nucleotidyltransferase
-
-
-
-
DNA-dependent RNA polymerase
nucleotidyltransferase, ribonucleate
-
-
-
-
Pol II
ribonucleate nucleotidyltransferase
-
-
-
-
ribonucleate polymerase
-
-
-
-
ribonucleic acid formation factors, C
-
-
-
-
ribonucleic acid nucleotidyltransferase
-
-
-
-
ribonucleic acid polymerase
-
-
-
-
ribonucleic acid transcriptase
-
-
-
-
ribonucleic polymerase
-
-
-
-
ribonucleic transcriptase
-
-
-
-
RNA formation factors, C
-
-
-
-
RNA nucleotidyltransferase
-
-
-
-
RNA nucleotidyltransferase (DNA-directed)
-
-
-
-
RNA polymerase
RNA polymerase I
-
-
-
-
RNA polymerase II
-
-
-
-
RNA polymerase III
-
-
-
-
RNA transcriptase
-
-
-
-
RNAP
RNAP I
-
-
-
-
RNAP II
-
-
-
-
RNAP III
-
-
-
-
transcriptase
-
-
-
-
DNA-dependent RNA polymerase
-
-
-
-
Pol II
-
-
-
-
RNA polymerase
-
-
-
-
RNAP
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleotidyl group transfer
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed)
Catalyses DNA-template-directed extension of the 3'- end of an RNA strand by one nucleotide at a time. Can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. See also EC 2.7.7.19 (polynucleotide adenylyltransferase) and EC 2.7.7.48 (RNA-directed RNA polymerase).
CAS REGISTRY NUMBER
COMMENTARY
9014-24-8
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
the enzyme requires DNA as template
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
a kind of transcription complex is formed during RNA polymerase catalysed synthesis of the M13 bacteriophage replication primer. The complex contains an overextended RNADNA hybrid bound in the RNA-polymerase through that is normally occupied by downstream double-stranded DNA, thus leaving the 30 end of the RNA available for interaction with DNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
enzyme is responsible for transcription in bacteria
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
regulation by anions, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression, synthesis of RNA transcripts of many thousands of nucleotides without dissociation. Energy, in the form of nucleoside triphosphates, fuels the synthesis of an RNA polymer complementary to specific regions of the DNA template. Like all macromolecular synthesis, RNA synthesis can be divided into three general phases: initiation, elongation, and termination. Importantly, each of these phases can be a target of regulation. Promoter recognition, binding at the extended promoter recognition region, and transcript initiation, RNAP prefers to initiate transcription within a narrow window located between 6 and 9 bp downstream of the -10 element, promoter clearance and elongation, termination and recycling, mechanisms and regulation , overview. The process of start site selection can be governed by the availability of either the +1 or the +2 NTP, depending on the promoter
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is DNA, native or denatured, method evaluation: specificity and extent of transcription depends strongly on the quality of the DNA preparation, the strength of the promoter and terminator sequences, and the kind and concentration of mono- and divalent cations in the reaction mixture
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
template is supercoiled DNA
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
the alpha subunit C-terminal domain of Escherichia coli RNA polymerase (alphaCTD) recognizes the upstream promoter(UP) DNA element via its characteristic minor groove shape and electrostatic potential
-
-
?
additional information
?
-
-
dinucleoside teraphosphates are more potent substrates than dinucleoside triphosphates and dinucleoside pentaphosphates
-
-
?
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
?
additional information
?
-
-
RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview
-
-
?
additional information
?
-
-
the core enzyme, which lacks the sigma subunit, synthesizes short transcripts relatively uniformly on the DNA template in the presence of high concentrations of random primers and low NTP concentrations
-
-
?
additional information
?
-
-
dsDNA templates used for activity are T7A1_763, T7A1_437, T7A1_149, pcDNA3.1, pGEM, T-phage DNA, Escherichia coli DNA, calf thymus DNA, poly(dA-dT), and Kool NC-45
-
-
?
additional information
?
-
-
RNA polymerase binds multiple sites in the ehxCABD gene regulatory region. At the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter -10 element and similar overlapping sequences. RNA polymerase competes with itself for binding to AT-rich sequences overlapping PehxCABD, correct positioning of RNA polymerase at PehxCABD requires H-NS
-
-
?
additional information
?
-
the subunits interact with recombinant His6-tagged CedA, a multi-copy suppressor which represses the dnaAcos inhibition of cell division. Determination of the binding site of CedA for RNA polymerase. The N-terminus of CedA is necessary for a tight interaction
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
a kind of transcription complex is formed during RNA polymerase catalysed synthesis of the M13 bacteriophage replication primer. The complex contains an overextended RNADNA hybrid bound in the RNA-polymerase through that is normally occupied by downstream double-stranded DNA, thus leaving the 30 end of the RNA available for interaction with DNA polymerase
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
enzyme is responsible for transcription in bacteria
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
regulation by anions, overview
-
-
?
nucleoside triphosphate + RNAn
diphosphate + RNAn+1
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression, synthesis of RNA transcripts of many thousands of nucleotides without dissociation. Energy, in the form of nucleoside triphosphates, fuels the synthesis of an RNA polymer complementary to specific regions of the DNA template. Like all macromolecular synthesis, RNA synthesis can be divided into three general phases: initiation, elongation, and termination. Importantly, each of these phases can be a target of regulation. Promoter recognition, binding at the extended promoter recognition region, and transcript initiation, RNAP prefers to initiate transcription within a narrow window located between 6 and 9 bp downstream of the -10 element, promoter clearance and elongation, termination and recycling, mechanisms and regulation , overview. The process of start site selection can be governed by the availability of either the +1 or the +2 NTP, depending on the promoter
-
-
?
additional information
?
-
-
multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions
-
-
?
additional information
?
-
-
RNA polymerase binds multiple sites in the ehxCABD gene regulatory region. At the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter -10 element and similar overlapping sequences. RNA polymerase competes with itself for binding to AT-rich sequences overlapping PehxCABD, correct positioning of RNA polymerase at PehxCABD requires H-NS
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Zinc
-
a conserved zinc binding domain in the largest subunit of DNA-dependent RNA polymerase modulates intrinsic transcription termination and antitermination but does not stabilize the elongation complex
Mg2+
-
the active center of the enzyme involves a symmetrical pair of Mg2+ ions that switch roles in synthesis and degradation. One ion is retained permanently and the other is recruited ad hoc for each act of catalysis. The weakly bound Mg2+ is stabilized in the active center in different modes depending on the type of reaction: during synthesis by the beta,gamma-phosphates of the incoming substrate and during hydrolysis by the phosphates of a non-base-paired nucleoside triphosphate
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(S)-2-((1-amino-1-oxo-3-phenylpropan-2-ylamino)methyl)-3-(4-amino phenoxy)-5-methoxy phenyl acetate
-
-
(S)-2-((1-amino-1-oxo-3-phenylpropan-2-ylamino)methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
-
-
(S)-2-((1-amino-3-(4-hydroxyphenyl)-1-oxopropan-2-ylamino)methyl)-3-(4-aminophenoxy)-5-methoxyphenyl acetate
-
-
(S)-2-((1-amino-3-(4-hydroxyphenyl)-1-oxopropan-2-ylamino)methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
-
-
1-[2-[3-(4-Chloro-3-trifluoromethylphenyl)ureido]-4-trifluoromethyl phenoxy]-4,5-dichlorobenzene sulfonic acid
-
-
2-([[(1S)-2-amino-1-(4-hydroxybenzyl)-2-oxoethyl]amino]methyl)-5-methoxy-3-(4-nitrophenoxy)phenyl acetate
-
-
4-[2-([[(1S)-2-amino-1-(4-hydroxybenzyl)ethyl]amino]methyl)-5-methoxy-3-(2-oxopropyl)benzyl]benzaldehyde
-
-
CBR703
-
the IC50s values are significantly decreased with template Kool NC-45, or increased with template poly(dA-dT)
d(Ap4C)
-
d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
d(Ap4G)
-
d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
d(Ap4T)
-
d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
d(Tp4C)
-
d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
d(Tp4T)
-
d(Ap4T), d(Ap4C) and d(Ap4G) inhibit the incorporation of dATP into DNA less effectively than d(Ap4T), d(Tp4T) and d(Tp4C) the dTTP incorporation
etnangien
-
from the myxobacterium Sorangium cellulosum, a poly-unsaturated 22-membered polyketide macrolide, inhibits bacterial RNA polymerase, shows no cross-resistance to rifampicin, poor inhibition
myxopyronin
-
an alpha-pyrone antibiotic, targets the RNAP switch region, which is the hinge that mediates opening and closing of the RNAP active-center cleft. Lower values for inhibition by myxopyronin in the presence of template Kool NC-45
protein gp76
-
the Thermus phage protein gp76 inhibits Escherichia coli RNAP highlighting the template-DNA binding site as a target site for developing antibacterial agents
-
additional information
-
despite relatively high overall sequence and structural homology between bacterial and mammalian core RNAP enzymes, there are sufficient differences between the enzyme classes for exploitation in the discovery of selective bacterial inhibitors
-
additional information
-
synthesis of simplified etnangien analogues and analysis of their antimicrobial activities, overview
-
additional information
-
the use of dsDNA templates containing classical promoters has only a negligible effects on the potency of enzyme inhibitors
-
additional information
-
FLiZ antagonize sigmaS-dependent gene expression in Escherichia coli. FliZ is an abundant DNA-binding protein and a global regulatory protein under the control of the flagellar master regulator FlhDC. It inhibits gene expression mediated by sigmaS by recognizing operator sequences that resemble the -10 region of sigmaS-dependent promoter. FLiZ plays a pivotal role in the decision between alternative life-styles, i.e. FlhDC-controlled flagellum-based motility or pS-dependent curli fimbriae-mediated adhesion and biofilm formation. FliZ is a global repressor with a DNA sequence specificity overlapping that of sigmaScontaining RNA polymerase, mechanism, overview
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
glutamate
-
glutamate remodels the sigma38 transcription complex for activation. Accumulation of the simple signaling molecule glutamate can reprogram RNA polymerase in vitro without the need for specific protein receptors. During osmotic activation, glutamate appears to act as a Hofmeister series osmolyte to facilitate promoter escape. Escape is accompanied by a remodeling of the key interaction between the sigma38 stress protein and the beta-flap of the bacterial core RNA polymerase. This activation event contrasts with the established mechanism of inhibition in which glutamate, by virtue of its electrostatic properties, helps to inhibit binding to ribosomal promoters after osmotic shock
histone-like nucleoid structuring protein
-
i.e. H-NS, H-NS stimulates transcription from the F3 fragment, it can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions. Correct positioning of RNA polymerase at PehxCABD requires H-NS. Footprint of RNA polymerase (s70 RC461-FeBABE) interactions with -10 elements in the ehxCABD regulatory region in the presence of H-NS, overview
-
potassium glutamate
-
activates highly, role of potassium ion in the activation of osmotic transcription
Rho
-
in response to the Rho termination factor, RNA synthesis ceases and the completed transcript is released
-
sigma factor
-
a dissociable specificity sigma factor, regulated by factors such as anti-sigma factors, which can sequester r factors and prevent core association, and possibly by factors that enhance sigma-core association
-
sigma70
-
the sigma factor increases the transcription efficiency of templates with nonphysiological nonprokaryotic promoters
-
additional information
-
interaction of elongation factors with RNAP, such as NusG and RfaH, affects the frequency and duration of pausing during transcription
-
additional information
-
RNAP contains the vegetative sigma subunit sigma70 (RpoD) and/or the flagellar sigma factor sigma28 (FliA)
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
assay for RNA polymerase activity that uses the dye RiboGreen to detect transcripts by fluorescence and is thus free of the expense, short shelf life, and high handling costs of radioisotopes. The method is relatively quick and can be performed entirely in microplate formate, allowing for the processing of dozens to hundreds of samples in parallel
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
643564, 643570, 643584, 643587, 660691, 661201, 662629, 663386, 673217, 676146, 702224, 702625, 703353, 703357, 705530, 706807, 706873, 721305, 723296, 761982, 761990, 762047
-
-
DNA-directed RNA polymerase subunits beta, beta', and alpha encoded by genes rpoC, rpoB, and rpoA; genes rpoC, rpoB, and rpoA
UniProt
P0A8T7: rpoC, DNA-directed RNA polymerase subunit beta, P0A8V2: rpoB, DNA-directed RNA polymerase subunit beta, P0A7Z4: rpoA, DNA-directed RNA polymerase subunit alpha, P0A800: rpoZ, DNA-directed RNA polymerase subunit omega
SwissProt
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug target
-
the template-DNA binding site is a target site for developing antibacterial agents
malfunction
-
reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation
physiological function
additional information
physiological function
-
RNAP is an exceptionally complex enzyme that can be thought of as the engine of gene expression
physiological function
-
the enzyme activates genes for high affinity nutrient scavenging and motility
physiological function
the enzyme subunits interact with CedA, a multi-copy suppressor which represses the dnaAcos inhibition of cell division. DnaAcos is a mutant of the initiator DnaA that causes overinitiation of chromosome replication in Escherichia coli resulting in inhibition of cell division. Determination of the binding site of CedA for RNA polymerase and examination of the binding functions involved in cell division reactivation
physiological function
gene transcription is carried out by multi-subunit RNA polymerase. Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Transcription bubble is stabilized by a helix separating the two DNA strands
physiological function
-
transcriptional bursting is caused by interplay between RNA polymerases on DNA
additional information
-
structure-based analysis of the evolution of archaeal and eukaryotic DNA-dependent RNA polymerases, overview
additional information
-
a single-molecule fluorescence assay is established to study bacterial transcription termination dynamics
additional information
-
RNA polymerase is a major target of gene regulation
additional information
-
studies on the transcription mechanism show transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
P0A8V4, A0A4S1NBU2, A0A073G207, A0A070UPX4
A0A073G207, A0A4S1NBU2, P0A802, P0A8V4
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
P0A8V4, A0A4S1NBU2, P0A802, A0A073G207
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
P0A8V4, A0A5F0PYH4, A0A659GYB8, T9C803
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
A0A073G207, A0A073H246, A0A4S1NBU2, P0A802
A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
P0A8V4, A0A073G207, P0A802, A0A4S1NBU2
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
P0A8V4, A0A4S1NBU2, P0A802, A0A073G207
A0A073G207, P0A802, P0A8V4, A0A4S1NBU2
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
A0A073G207, A0A4S1NBU2, P0A802, P0A8V4
A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
P0A8V4, A0A073G207, A0A4S1NBU2, P0A802
A0A073G207, P0A8V4, A0A4S1NBU2, P0A802
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
145000
-
betax,beta,sigma,alpha, x * 160000 + x * 145000 + x * 85000 + x * 40000, SDS-PAGE
160000
-
betax,beta,sigma,alpha, x * 160000 + x * 145000 + x * 85000 + x * 40000, SDS-PAGE
40000
-
betax,beta,sigma,alpha, x * 160000 + x * 145000 + x * 85000 + x * 40000, SDS-PAGE
85000
-
betax,beta,sigma,alpha, x * 160000 + x * 145000 + x * 85000 + x * 40000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
betax,beta,sigma,alpha, x * 160000 + x * 145000 + x * 85000 + x * 40000, SDS-PAGE
multimer
-
bacterial RNAP is a multisubunit enzyme and consists of a core polymerase containing the beta, beta' , and two alpha subunits, together with one or more omega subunits, and a dissociable specificity factor sigma
additional information
additional information
-
dimer-monomer formation is reversible and the equilibrium depends on the ionic strength of the medium. At high ionic strength the enzyme dissociates to a monomeric form
additional information
-
binding of the sigma70 subunit to the core enzyme induces conformational changes in a single-stranded DNA binding region of the protein. As a consequence of these conformational changes, sigma70 subunit gains the specificity for the nontemplate strand of the melted region in the open complex
additional information
-
the core of the procaryotic RNAP comprises five subunits
additional information
-
conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview
additional information
-
secondary structure and organization of multi-subunit DNA-dependent RNA polymerases, overview. The Rpb8/G RNA polymerase subunit is restricted to eukaryotes and Crenarchaea
additional information
-
RNAP contains the vegetative sigma subunit sigma70 (RpoD) and/or the flagellar sigma factor sigma28 (FliA)
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C70A/C72H/C85A/C88H
-
mutant enzyme is defective in intrinsic termination and antitermination in vitro. Mutation likely causes a recessive-lethal phenotype
C70H
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
C72H
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
C85H
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
del70-88insGGGG
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
del74-84insGGGG
-
mutant enzyme terminates more poorly than wild-type enzyme on put(-) templates, and responds weakly on put. Mutation likely causes a recessive-lethal phenotype
E813A/D814A
-
significantly decreased elongation rate, the mutation changes the effect of diphosphate on the 3'-5'-exonuclease reaction, whose addition stimulates the production of UMP through hydrolysis rather than of UTP through diphosphorolysis. The mutation makes the 3'-exonuclease activity independent of TTP. The mutation changes the response of TEC to diphosphate: instead of causing diphosphorolysis it stimulates the exonuclease reaction
R1106A
-
significantly decreased elongation rate, enhanced exonuclease activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
the genes rpoA, rpoB and rpoC which encode the RNA polymerase, alpha-, beta- and betasubunits, respectively, have been individually placed on expression plasmids under control of the bacteriophage T7 promoter. Induction of the T7 RNA polymerase gene in hist cells harbouring each of the three plasmids, results in the extensive overproduction of the three polypeptides
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
assay for RNA polymerase activity that uses the dye RiboGreen to detect transcripts by fluorescence and is thus free of the expense, short shelf life, and high handling costs of radioisotopes. The method is relatively quick and can be performed entirely in microplate formate, allowing for the processing of dozens to hundreds of samples in parallel
medicine
-
the enzyme is a promising target for the discovery of new antimicrobial agents
synthesis
-
the enzyme is useful for in vitro transcription reactions to produce preparative quantities of transcribed RNA and labeled RNA probes, method evaluation, overview
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Zalenskaya, K.; Lee, J.; Gujuluva, C.N.; Shin, Y.K.; Slutsky, M.; Goldfarb, A.
Recombinant RNA polymerase: inducible overexpression, purification and assembly of Escherichia coli rpo gene products
Gene
89
7-12
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Escherichia coli
Sethi, V.S.
Structure and function of DNA-dependent RNA-polymerase
Prog. Biophys. Mol. Biol.
23
67-101
1971
Escherichia coli
Imburgio, D.; Anikin, M.; McAllister, W.T.
Effects of substitutions in a conserved DX2GR sequence motif, found in many DNA-dependent nucleotide polymerases, on transcription by T7 RNA polymerase
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319
37-51
2002
Escherichia phage T7, Escherichia coli
Callaci, S.; Heyduk, T.
Conformation and DNA binding properties of a single-stranded DNA binding region of sigma 70 subunit from Escherichia coli RNA polymerase are modulated by an interaction with the core enzyme
Biochemistry
37
3312-3320
1998
Escherichia coli
Kuhlman, P.; Duff, H.L.; Galant, A.
A fluorescence-based assay for multisubunit DNA-dependent RNA polymerases
Anal. Biochem.
324
183-190
2004
Escherichia coli
Tan, X.X.; Chen, Y.
A novel genomic approach identifies bacterial DNA-dependent RNA polymerase as the target of an antibacterial oligodeoxynucleotide, RBL1
Biochemistry
44
6708-6714
2005
Escherichia coli
King, R.A.; Markov, D.; Sen, R.; Severinov, K.; Weisberg, R.A.
A conserved zinc binding domain in the largest subunit of DNA-dependent RNA polymerase modulates intrinsic transcription termination and antitermination but does not stabilize the elongation complex
J. Mol. Biol.
342
1143-1154
2004
Escherichia coli
Skoblov, A.Y.; Sosunov, V.V.; Victorova, L.S.; Skoblov, Y.S.; Kukhanova, M.K.
Substrate properties of dinucleoside 5',5''-oligophosphates in the reactions catalyzed by HIV reverse transcriptase, E. coli DNA polymerase I, and E. coli RNA polymerase
Russ. J. Bioorg. Chem.
31
48-57
2005
Escherichia coli
-
Chopra, I.
Bacterial RNA polymerase: a promising target for the discovery of new antimicrobial agents
Curr. Opin. Investig. Drugs
8
600-607
2007
Escherichia coli
Zenkin, N.; Naryshkina, T.; Kuznedelov, K.; Severinov, K.
The mechanism of DNA replication primer synthesis by RNA polymerase
Nature
439
617-620
2006
Escherichia coli
Gralla, J.D.; Huo, Y.X.
Remodeling and activation of Escherichia coli RNA polymerase by osmolytes
Biochemistry
47
13189-13196
2008
Escherichia coli
Menche, D.; Li, P.; Irschik, H.
Design, synthesis and biological evaluation of simplified analogues of the RNA polymerase inhibitor etnangien
Bioorg. Med. Chem. Lett.
20
939-941
2009
Corynebacterium glutamicum, Saccharomyces cerevisiae, Escherichia coli, Micrococcus luteus, Staphylococcus aureus, Mycolicibacterium phlei, Gordonia rubripertincta
Svetlov, V.; Nudler, E.
Macromolecular micromovements: how RNA polymerase translocates
Curr. Opin. Struct. Biol.
19
701-707
2009
Saccharomyces cerevisiae, Escherichia coli, Thermus thermophilus, Saccharolobus solfataricus, Thermus aquaticus
Paschal, B.M.; McReynolds, L.A.; Noren, C.J.; Nichols, N.M.
RNA polymerases
Curr. Protoc. Mol. Biol.
Chapter 3
Unit3.8
2008
Enterobacteria phage T3, Escherichia phage T7, Escherichia coli, Zindervirus SP6
Helmann, J.D.
RNA polymerase: a nexus of gene regulation
Methods
47
1-5
2009
Bacillus subtilis, Escherichia coli
Agarwal, A.; Johnson, A.; Fishwick, C.
Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase
Tetrahedron
64
10049-10054
2008
Escherichia coli, Thermus aquaticus
-
Kwapisz, M.; Beckouet, F.; Thuriaux, P.
Early evolution of eukaryotic DNA-dependent RNA polymerases
Trends Genet.
24
211-215
2008
Saccharomyces cerevisiae, Cenarchaeum symbiosum, Escherichia coli, Emiliania huxleyi, Methanocaldococcus jannaschii, Pyrococcus furiosus, Sulfolobus acidocaldarius, Saccharolobus solfataricus, Nanoarchaeum equitans, Caldivirga maquilingensis, Nitrosopumilus maritimus, Thermofilum pendens
Haupenthal, J.; Huesecken, K.; Negri, M.; Maurer, C.K.; Hartmann, R.W.
Influence of DNA template choice on transcription and inhibition of Escherichia coli RNA polymerase
Antimicrob. Agents Chemother.
56
4536-4539
2012
Escherichia coli
Pesavento, C.; Hengge, R.
The global repressor FliZ antagonizes gene expression by sigmaS-containing RNA polymerase due to overlapping DNA binding specificity
Nucleic Acids Res.
40
4783-4793
2012
Escherichia coli
Abe, Y.; Fujisaki, N.; Miyoshi, T.; Watanabe, N.; Katayama, T.; Ueda, T.
Functional analysis of CedA based on its structure: residues important in binding of DNA and RNA polymerase and in the cell division regulation
J. Biochem.
159
217-223
2016
Escherichia coli (P0A8T7 AND P0A8V2 AND P0A7Z4)
Singh, S.S.; Grainger, D.C.
H-NS can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions
PLoS Genet.
9
e1003589
2013
Escherichia coli
Lara-Gonzalez, S.; Dantas Machado, A.C.; Rao, S.; Napoli, A.A.; Birktoft, J.; Di Felice, R.; Rohs, R.; Lawson, C.L.
The RNA polymerase alpha subunit recognizes the DNA shape of the upstream promoter element
Biochemistry
59
4523-4532
2020
Escherichia coli (P0A7Z4), Escherichia coli K12 (P0A7Z4)
Glyde, R.; Ye, F.; Jovanovic, M.; Kotta-Loizou, I.; Buck, M.; Zhang, X.
Structures of bacterial RNA polymerase complexes reveal the mechanism of DNA loading and transcription initiation
Mol. Cell
70
1111-1120
2018
Escherichia coli (P0A8T7 AND P0A8V2 AND P0A7Z4 AND P0A800), Escherichia coli K12 (P0A8T7 AND P0A8V2 AND P0A7Z4 AND P0A800)
Kang, W.; Ha, K.S.; Uhm, H.; Park, K.; Lee, J.Y.; Hohng, S.; Kang, C.
Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA
Nat. Commun.
11
450
2020
Escherichia coli
Fujita, K.; Iwaki, M.; Yanagida, T.
Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA
Nat. Commun.
7
13788
2016
Escherichia coli
Ooi, W.Y.; Murayama, Y.; Mekler, V.; Minakhin, L.; Severinov, K.; Yokoyama, S.; Sekine, S.I.
A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation
Nucleic Acids Res.
46
431-441
2018
Escherichia coli, Thermus thermophilus (Q5SHR6 AND Q8RQE9 AND Q8RQE8 AND Q8RQE7)
EXTERNAL LINKS (specific for EC-Number 2.7.7.6)
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